I am working on a project to install 100+ nodes of temperature sensors in an area, all of which perform the same function. The data they publish is the sensor id and the reading
It would seem that the only way to do that would be to create your own gateway that aggregates the data before sending it to AWS IoT. You can't have multiple MQTT connections with the same client ID.
Use the API to automate assignment of certificates and private keys to nodes. The sensor ID may be used as the thing name and MQTT client ID. It takes some work up front, but then you can leverage AWS IoT for all the housekeeping moving forward.